I am having a scored bed file with weighted values in the 4th column. I want to use this scored file to as a sorting parameter for another .bam file. However, the input to computeMatrix operation allows only bigWig files to be used in -S option...and creating bigWig files required indexing based on chr# due to which the ranking is lost.
How can I sort the heatmap with a scored BED file ?
computeMatrix reference-point --referencePoint TSS -a 10 -b 10 -bs 2 -p max --sortRegions keep -R UCSC_Main_on_Human_refGene_hg19_TSS.txt -S 8min_sorter_final.bw -out 8min_sorter_final.txt.gz plotHeatmap -m 8min_sorter_final.txt.gz \ -out 8min_sorter_final.png \ --colorList white,blue \ --missingDataColor 0 \ --heatmapHeight 40 \ --sortRegions no \ --heatmapWidth 10
This gives completely unsorted heatmap.
I am not sure if I am missing something obvious, but I really cant see a way to use a sorted BED file as a direct parameter to sort the matrix generated by computeMatrix. FWIW, I am using Deeptools 2.